from pathlib import Path
import argparse
from .openpvs1 import OpenPVS1


def main():
    parser = argparse.ArgumentParser(description="AutoPVS1 Batch")
    parser.add_argument("--input_files", "-in", nargs="+", type=Path, required=True, help="input VCF file")
    parser.add_argument("--output_file", "-out", type=Path, required=True, help="output VCF file")
    parser.add_argument("--genome_file", "-genome", type=Path, required=True, help="genome FASTA file")
    parser.add_argument("--genome_builder", "-build", choices=("hg19", "hg38"), required=True, help="genome builder version")
    parser.add_argument("--data_dir", "-data", type=Path, default=Path(__file__).parent / "data", help="data directory")
    parser.set_defaults(func=lambda args: OpenPVS1(**vars(args)).run())
    args = parser.parse_args()
    args.func(args)
